RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780806|ref|YP_003065219.1| chromosome partitioning
protein A [Candidatus Liberibacter asiaticus str. psy62]
(265 letters)
>gnl|CDD|31385 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 220 bits (560), Expect = 4e-58
Identities = 112/261 (42%), Positives = 158/261 (60%), Gaps = 4/261 (1%)
Query: 5 KSRIITIANQKGGVGKTTTAINLSTALA-AIGENVLLIDLDPQGNASTGLGIELYDRKYS 63
+II +ANQKGGVGKTTTA+NL+ ALA G+ VLLIDLDPQG+ ++ LG+ D +
Sbjct: 1 MMKIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRP-DLEGD 59
Query: 64 SYDLLIEEKNINQILIQT-AIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTS 122
Y+LL K IL T I L +IPS +DL I + L + L +
Sbjct: 60 LYNLLSGLKERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLD-PVKD 118
Query: 123 DFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALD 182
D+ YI +D PPS +LT+NA+AAAD +L+P+Q EF LEGL QLL T+E++ + + L
Sbjct: 119 DYDYIIIDTPPSLGVLTLNALAAADHVLIPVQPEFLDLEGLEQLLNTLEDLLKLRRNKLI 178
Query: 183 IQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCA 242
+ GI++T FDSR L+ +V+ ++++ LG V T IPR V EA + GKP YD K
Sbjct: 179 VVGILITRFDSRTKLADEVLQELKQLLGDPVLKTKIPRRVAYREAAAEGKPLYEYDPKSK 238
Query: 243 GSQAYLKLASELIQQERHRKE 263
++ Y +LA EL+++ K
Sbjct: 239 AAEEYYELAKELLEELLKLKP 259
>gnl|CDD|145019 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyse amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well as
the plasmid partitioning proteins of the MinD/ParA
family.
Length = 212
Score = 142 bits (359), Expect = 1e-34
Identities = 78/228 (34%), Positives = 112/228 (49%), Gaps = 26/228 (11%)
Query: 9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGN--ASTGLGIELYDR-KYSSY 65
I IA KGGVGKTT A NL+ ALA G VLLIDLDPQ N +S G G +L D K
Sbjct: 1 IAIAGTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANLTSSLGKGPDLIDVLKEGLE 60
Query: 66 DLLIEEKNINQILIQT--AIPNLSIIPSTMDLLG--IEMILGGEKDRLFRLDKALSVQLT 121
+ + I + L +IPS + L E+IL G ++ L +L
Sbjct: 61 IVDAQPLQHIAAAIVPSRNLDPLLLIPSNLSLANFESELILEGGEEGLIKL--------- 111
Query: 122 SDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSAL 181
+ Y+ +D P LT NA+ AAD ++VP++ E A+ G +LLE VE + L
Sbjct: 112 -AYDYVIIDGAPGLGELTANALVAADILVVPIEPEGVAVLGAQRLLELVERLG------L 164
Query: 182 DIQGIILTMFDSRN-SLSQQVVSDVRKNLGG--KVYNTVIPRNVRISE 226
I G++L D + + + + + G + VIPR++ +SE
Sbjct: 165 KILGVVLNKVDRGDERHLDKEIEALERKTGIPVLLLLGVIPRDLALSE 212
>gnl|CDD|30803 COG0455, COG0455, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 262
Score = 100 bits (250), Expect = 5e-22
Identities = 62/254 (24%), Positives = 117/254 (46%), Gaps = 16/254 (6%)
Query: 5 KSRIITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDPQ-GNASTGLGIELYDRKY 62
+++I + + KGGVGKTT NL ALAA+ G+ VLLID D GN S LG+E +
Sbjct: 1 MTKVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLIDADLGLGNLSLLLGVE--SKPT 58
Query: 63 SSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTS 122
+ +D+L E +I I+ +T L ++P L + + + + + + +L
Sbjct: 59 TLHDVLAGEASIEDIIYETPQDGLYVLPGGSGLEDLAKLDPEDLEDVIK-------ELEE 111
Query: 123 DFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALD 182
+ YI +D + T++ + ++D +++ E ++ + ++ + + L
Sbjct: 112 LYDYILIDTGAGLSRDTLSFILSSDELVIVTTPEPTSITDAYKTIKIL----SKLGLDLL 167
Query: 183 IQGIILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCA 242
+ ++L S ++ V VIP + + A + GKP ++Y
Sbjct: 168 GRRVVLNRVRSTKEGVDVAALLIQVVKQVPVLQ-VIPFDPEVRRALAEGKPIVLYSPNSK 226
Query: 243 GSQAYLKLASELIQ 256
SQA +LA++L
Sbjct: 227 ASQAIKELAAKLAG 240
>gnl|CDD|73299 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer..
Length = 179
Score = 78.3 bits (193), Expect = 2e-15
Identities = 58/240 (24%), Positives = 92/240 (38%), Gaps = 61/240 (25%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDL 67
+I + + KGGVGKTTT NL TALA +G V+LID D
Sbjct: 1 VIVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADL---------------------- 38
Query: 68 LIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYI 127
+ NL +ILG E ++ L L+ YI
Sbjct: 39 --------------GLRNLD------------LILGLENRVVYTLHDVLAGD------YI 66
Query: 128 FLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGII 187
+D P + A+A AD L+ E +L ++ +E + + + G+I
Sbjct: 67 LIDSPAGIERGFITAIAPADEALLVTTPEISSLRDADRVKGLLEAL------GIKVVGVI 120
Query: 188 LTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQAY 247
+ +V D+ + LG + VIP + + A + G+P ++ K +QAY
Sbjct: 121 VNRVRPDMVEGGDMVEDIEEILGVPLLG-VIPEDPAVIRATNRGEPVVLNKPKSPAAQAY 179
>gnl|CDD|32719 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 75.2 bits (185), Expect = 2e-14
Identities = 73/264 (27%), Positives = 124/264 (46%), Gaps = 23/264 (8%)
Query: 6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDRK--Y 62
+RII + + KGGVGKTTT N+ TALA +G+ V+LID D N +G+E + Y
Sbjct: 2 ARIIVVTSGKGGVGKTTTTANIGTALAQLGKKVVLIDFDIGLRNLDLIMGLE---NRIVY 58
Query: 63 SSYDLLIEEKNINQILIQTA-IPNLSIIPSTMDLLGIEMILGGEKDRLFR--LDKALSVQ 119
D++ E +NQ LI+ + NL ++P++ +KD L + K ++
Sbjct: 59 DLVDVIEGEATLNQALIKDKRLENLFLLPASQT---------RDKDALTPEGVKKVVNEL 109
Query: 120 LTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVE-EVRRTVN 178
DF YI +D P NA+ AD +V E ++ +++ +E + RR
Sbjct: 110 KAMDFDYIIIDSPAGIEQGFKNAVYFADEAIVVTNPEVSSVRDSDRIIGLLESKSRRAEI 169
Query: 179 SALDIQGIILTMFDSRNSLSQQVVS--DVRKNLGGKVYNTVIPRNVRISEAPSYGKPAII 236
+ ++L + +++S DV + L + VIP + + A + G+P +I
Sbjct: 170 GEEPKEHLLLNRYRPEMVKRGEMLSVEDVLEILSIPLIG-VIPEDQDVLRASNKGEP-VI 227
Query: 237 YDLKCAGSQAYLKLASELIQQERH 260
D +AY +A L+ +E
Sbjct: 228 LDDNSDAGKAYRDIARRLLGEEVP 251
>gnl|CDD|73302 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to
a conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase
activity by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its
DNA binding sites. Increasing the fraction of ParA-ADP
in the cell inhibits cell division, suggesting that
this simple nucleotide switch may regulate cytokinesis.
ParA shares sequence similarity to a conserved and
widespread family of ATPases which includes the repA
protein of the repABC operon in R. etli Sym plasmid.
This operon is involved in the plasmid replication and
partition..
Length = 104
Score = 71.4 bits (175), Expect = 2e-13
Identities = 29/39 (74%), Positives = 34/39 (87%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
+I +ANQKGGVGKTTTA+NL+ ALA G+ VLLIDLDPQ
Sbjct: 1 VIAVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLDPQ 39
Score = 68.4 bits (167), Expect = 2e-12
Identities = 34/76 (44%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 114 KALSVQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEV 173
+ L + L + YI +D PPS LLT NA+AAAD +L+P+Q L+GL +LLET +
Sbjct: 30 RVLLIDLDPQYDYIIIDTPPSLGLLTRNALAAADLVLIPVQPSPLDLDGLEKLLET-LIL 88
Query: 174 RRTVNSALDIQGIILT 189
+N LDI GI+ T
Sbjct: 89 EDRLNPDLDILGILPT 104
>gnl|CDD|164554 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 61.7 bits (150), Expect = 2e-10
Identities = 50/153 (32%), Positives = 78/153 (50%), Gaps = 12/153 (7%)
Query: 2 EEKKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD-PQGNASTGLGIELYDR 60
SRII I + KGGVGKTTT NL ++A +G V LID D N LG+E +R
Sbjct: 11 SATMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDADIGLRNLDLLLGLE--NR 68
Query: 61 -KYSSYDLLIEEKNINQILIQTA-IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSV 118
Y++ D+L E ++Q LI+ NLS++ + + + + + L +L
Sbjct: 69 VLYTAMDVLEGECRLDQALIRDKRWKNLSLLAISKNRQRYNV----TRKNMNMLVDSLKN 124
Query: 119 QLTSDFSYIFLDCPPSFNLLTMNAMAAADSILV 151
+ + YI +DCP ++ +NA+A A +V
Sbjct: 125 R---GYDYILIDCPAGIDVGFINAIAPAQEAIV 154
>gnl|CDD|30835 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 59.3 bits (143), Expect = 1e-09
Identities = 49/190 (25%), Positives = 86/190 (45%), Gaps = 25/190 (13%)
Query: 7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSSY 65
+I + + KGGVGK+T A+NL+ ALA +G+ VLL+D D +G + LG+E
Sbjct: 58 NVIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDADLRGPSIPRMLGLENLPGLTE-- 115
Query: 66 DLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGG---EKDRLFRLDKALSVQLTS 122
L+ + + ++ I LSI+P L + +I G K L L+ L
Sbjct: 116 --LLAGEALEPVIQHDGIKVLSILP----LGPVPVIPRGLLGSKAMLQLLEDVLW----G 165
Query: 123 DFSYIFLDCPPSFNL--LTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSA 180
++ Y+ +D PP T+ ++V ALE + + ++ +E+
Sbjct: 166 EYDYVIIDTPPGTGDADATVLQRIPDGVVIVTTP-GKTALEDVKKAIDMLEKAGI----- 219
Query: 181 LDIQGIILTM 190
+ G++ M
Sbjct: 220 -PVLGVVENM 228
>gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence..
Length = 217
Score = 52.2 bits (125), Expect = 2e-07
Identities = 30/126 (23%), Positives = 44/126 (34%), Gaps = 2/126 (1%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNI 74
KGGVGKTT A + LA G+ VLL+ DP N S L D +
Sbjct: 7 KGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPEIAPNLYR 66
Query: 75 NQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQLTSDFSYIFLDCPPS 134
++ + + L + G E+ L L + I D P+
Sbjct: 67 EEVDATRRVERAWGGEGGLMLELAAALPGIEE--LASLLAVFREFSEGLYDVIVFDTAPT 124
Query: 135 FNLLTM 140
+ L +
Sbjct: 125 GHTLRL 130
>gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 51.5 bits (123), Expect = 2e-07
Identities = 38/134 (28%), Positives = 58/134 (43%), Gaps = 9/134 (6%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL-YDRKYSSYDLLIEEKN 73
KGGVGKTT A + LA G+ VLL+ DP + +EL +D + +L E +
Sbjct: 10 KGGVGKTTIAAATAVKLAESGKKVLLVSTDPAHSLGDVFDLELGHDPRKVGPNLDALELD 69
Query: 74 INQIL---IQTAIPNLSIIPSTMDLLGIEM----ILGGEKDRLFRLDKALSVQLTSDFSY 126
+ L L+ + T L GI L G D L K L ++ ++
Sbjct: 70 PEKALEEYWDEVKDYLARLLRTRGLGGIYADELATLPG-IDEALALLKILEYYVSGEYDV 128
Query: 127 IFLDCPPSFNLLTM 140
I +D P+ + L +
Sbjct: 129 IVVDTAPTGHTLRL 142
>gnl|CDD|38232 KOG3022, KOG3022, KOG3022, Predicted ATPase, nucleotide-binding
[Cell cycle control, cell division, chromosome
partitioning].
Length = 300
Score = 50.3 bits (120), Expect = 5e-07
Identities = 59/272 (21%), Positives = 111/272 (40%), Gaps = 44/272 (16%)
Query: 6 SRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQG-NASTGLGIELYDRKYSS 64
II + + KGGVGK+T +NL+ ALA+ G+ V L+D D G + +G+E
Sbjct: 47 KHIILVLSGKGGVGKSTVTVNLALALASEGKKVGLLDADLCGPSIPRMMGLE-------- 98
Query: 65 YDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDR-LFRLDKALSV--QLT 121
+++ + N ++ NL L+ + +L D ++R K S+ Q
Sbjct: 99 GEVVHQSDNGWIPVVVN--KNLK-------LMSMGFLLKPRDDSVIWRGPKKNSMIKQFL 149
Query: 122 SD-----FSYIFLDCPPSFN---LLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEV 173
D Y+ +D PP + L + + +D ++ + A L + +E+
Sbjct: 150 KDVDWGELDYLVIDTPPGTSDEHLSLVQFLRESDGAVIVTTPQEVA------LQDVRKEI 203
Query: 174 RRTVNSALDIQGIILTMF--------DSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRIS 225
+ + I G++ M S N + + LG +P + I+
Sbjct: 204 DFCRKAGIPILGVVENMSGFVCPKCGHSTNIFGSGGGERLAEELGLP-LLGSLPLDPLIA 262
Query: 226 EAPSYGKPAIIYDLKCAGSQAYLKLASELIQQ 257
E+ G P + S+A+ +A +L++Q
Sbjct: 263 ESSDSGVPFVEEYPDSPASEAFEDIAEKLVEQ 294
>gnl|CDD|73300 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is
a homologue of the Fer4_NifH superfamily. Like the
other members of the superfamily, MRP contains a
ATP-binding domain at the N-termini. It is found in
bacteria as a membrane-spanning protein and functions
as a Na+/H+ antiporter..
Length = 169
Score = 50.5 bits (121), Expect = 5e-07
Identities = 19/37 (51%), Positives = 27/37 (72%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
+I + + KGGVGK+T A+NL+ ALA +G V L+D D
Sbjct: 1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKVGLLDAD 37
>gnl|CDD|73301 cd02038, FleN-like, FleN is a member of the Fer4_NifH
superfamily. It shares the common function as an
ATPase, with the ATP-binding domain at the N-terminus.
In Pseudomonas aeruginosa, FleN gene is involved in
regulating the number of flagella and chemotactic
motility by influencing FleQ activity..
Length = 139
Score = 50.1 bits (120), Expect = 7e-07
Identities = 20/37 (54%), Positives = 27/37 (72%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
II + + KGGVGKT + NL+ ALA +G+ VLL+D D
Sbjct: 1 IIAVTSGKGGVGKTNISANLALALAKLGKRVLLLDAD 37
>gnl|CDD|34570 COG4963, CpaE, Flp pilus assembly protein, ATPase CpaE
[Intracellular trafficking and secretion].
Length = 366
Score = 48.8 bits (116), Expect = 1e-06
Identities = 40/179 (22%), Positives = 80/179 (44%), Gaps = 16/179 (8%)
Query: 4 KKSRIITIANQKGGVGKTTTAINLSTALAA-IGENVLLIDLD-PQGNASTGLGIELYDRK 61
++ R + KGGVG +T A NL+ LA G VLL+DLD G A+ L +
Sbjct: 102 QQGRELAFLGAKGGVGTSTLAHNLAKGLAILSGAAVLLVDLDLQGGTAALYLDQDP---A 158
Query: 62 YSSYDLLIEEKNINQILIQTA----IPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALS 117
+ + + + + ++Q+L+ + L ++ + +L + G +R L
Sbjct: 159 FGIAEAVKQPERLDQVLLDSLLTRLASGLKLLAAPTELAKNYDLKTGAVER-------LL 211
Query: 118 VQLTSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRT 176
L F ++ +D P + T ++ +D I++ + +L +LL+ ++ +R
Sbjct: 212 DLLRGSFDFVVVDLPNIWTDWTRQVLSGSDEIVIVAEPSLASLRNAKELLDELKRLRPN 270
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 47.0 bits (111), Expect = 6e-06
Identities = 21/35 (60%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAIGENVLLID 42
+I + KGGVGKTT A NL+ ALA G+ VLLID
Sbjct: 1 VIVVTG-KGGVGKTTLAANLAAALAKRGKRVLLID 34
Score = 33.9 bits (77), Expect = 0.051
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 126 YIFLDCPPSFNLLTM---NAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALD 182
Y+ +D PP LL + A+ AAD +++ E A+ G E V L
Sbjct: 36 YVLIDTPPGLGLLVLLCLLALLAADLVIIVTTPEALAVLG---ARRLTEVVLELAIEGLR 92
Query: 183 IQGIILT 189
G+++
Sbjct: 93 PVGVVVN 99
>gnl|CDD|73340 cd03111, CpaE_like, This protein family consists of proteins
similar to the cpaE protein of the Caulobacter pilus
assembly and the orf4 protein of Actinobacillus pilus
formation gene cluster. The function of these proteins
are unkown. The Caulobacter pilus assembly contains 7
genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF.
These genes are clustered together on chromosome..
Length = 106
Score = 45.7 bits (108), Expect = 1e-05
Identities = 22/40 (55%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 8 IITIANQKGGVGKTTTAINLSTALAAI-GENVLLIDLDPQ 46
+I KGGVG TT A NL+ ALA G VLL+DLD Q
Sbjct: 1 VIAFIGAKGGVGATTLAANLAVALAKEAGRRVLLVDLDLQ 40
>gnl|CDD|73339 cd03110, Fer4_NifH_child, This protein family's function is unkown.
It contains nucleotide binding site. It uses NTP as
energy source to transfer electron or ion..
Length = 179
Score = 44.8 bits (106), Expect = 2e-05
Identities = 40/205 (19%), Positives = 73/205 (35%), Gaps = 41/205 (20%)
Query: 9 ITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLL 68
I + + KGG GKTT ++ ALAA+ +NV+L D D
Sbjct: 2 IAVISGKGGTGKTT----VTAALAALLKNVVLADCD------------------------ 33
Query: 69 IEEKNINQILIQTAIPNLSIIPST-----MDLLGIEMILGGEKDRLFRLDKALSVQLTSD 123
++ N++ L I L I L G+ R A +
Sbjct: 34 VDAPNLHLFLKPEIEEEEDFIVGGKKAVIDPELCISCGLCGKLVTEVR-KHAKEIAKAEG 92
Query: 124 FSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDI 183
I +D PP + ++ AD+ L+ + L L + +E V V
Sbjct: 93 AELIIIDGPPGIGCPVIASLTGADAALLVTEPTPSGLHDLERAVELVRHFGIPV------ 146
Query: 184 QGIILTMFDSRNSLSQQVVSDVRKN 208
G+++ +D + +++++ +
Sbjct: 147 -GVVINKYDLNDEIAEEIEDYCEEE 170
>gnl|CDD|48371 cd02117, NifH_like, This family contains the NifH (iron protein)
of nitrogenase, L subunit (BchL/ChlL) of the
protochlorophyllide reductase and the BchX subunit of
the Chlorophyllide reductase. Members of this family
use energey from ATP hydrolysis and transfer electrons
through a Fe4-S4 cluster to other subunit for reduction
of substrate..
Length = 212
Score = 44.8 bits (106), Expect = 2e-05
Identities = 18/32 (56%), Positives = 25/32 (78%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
KGG+GK+TT+ NLS ALA +G+ VL + DP+
Sbjct: 8 KGGIGKSTTSQNLSAALAEMGKKVLQVGCDPK 39
>gnl|CDD|31539 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 44.8 bits (106), Expect = 2e-05
Identities = 17/36 (47%), Positives = 29/36 (80%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
KGG+GK+TT+ NL+ ALA +G+ VL++ DP+ +++
Sbjct: 9 KGGIGKSTTSQNLAAALAELGKKVLIVGCDPKADST 44
Score = 34.4 bits (79), Expect = 0.033
Identities = 27/115 (23%), Positives = 55/115 (47%), Gaps = 7/115 (6%)
Query: 146 ADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQGIILTMFDSRNSLSQ-QVVSD 204
AD I + E AL + + + + + +T L GII +SR+ + ++V
Sbjct: 143 ADEIYIVTSGEMMALYAANNIAKGIRKYAKTGGVRL--GGII---CNSRSVDRERELVEA 197
Query: 205 VRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQAYLKLASELIQQER 259
+ LG ++ + +PR+ + +A GK I Y ++ Y +LA ++++ E+
Sbjct: 198 FAERLGTQLIH-FVPRDNIVQKAELNGKTVIEYAPDSNQAEEYRELAKKILENEK 251
>gnl|CDD|143913 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding
proteins, NifH/frxC family.
Length = 269
Score = 44.7 bits (106), Expect = 3e-05
Identities = 20/39 (51%), Positives = 29/39 (74%), Gaps = 1/39 (2%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL 53
KGG+GK+TT+ N S ALA +G+ VL++ DP+ + ST L
Sbjct: 8 KGGIGKSTTSQNTSAALAEMGKKVLIVGCDPKAD-STRL 45
>gnl|CDD|48363 cd02033, BchX, Chlorophyllide reductase converts chlorophylls
into bacteriochlorophylls by reducing the chlorin
B-ring. This family contains the X subunit of this
three-subunit enzyme. Sequence and structure similarity
between bchX, protochlorophyllide reductase L subunit
(bchL and chlL) and nitrogenase Fe protein (nifH gene)
suggest their functional similarity. Members of the
BchX family serve as the unique electron donors to
their respective catalytic subunits (bchN-bchB,
bchY-bchZ and nitrogenase component 1).
Mechanistically, they hydrolyze ATP and transfer
electrons through a Fe4-S4 cluster..
Length = 329
Score = 43.5 bits (102), Expect = 6e-05
Identities = 23/50 (46%), Positives = 33/50 (66%), Gaps = 1/50 (2%)
Query: 4 KKSRIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGL 53
KK++II I KGG+GK+ T NLS +A G+ VLLI DP+ + ++ L
Sbjct: 29 KKTQIIAIYG-KGGIGKSFTLANLSYMMAQQGKRVLLIGCDPKSDTTSLL 77
>gnl|CDD|48362 cd02032, Bchl_like, This family of proteins contains bchL and
chlL. Protochlorophyllide reductase catalyzes the
reductive formation of chlorophyllide from
protochlorophyllide during biosynthesis of chlorophylls
and bacteriochlorophylls. Three genes, bchL, bchN and
bchB, are involved in light-independent
protochlorophyllide reduction in bacteriochlorophyll
biosynthesis. In cyanobacteria, algae, and gymnosperms,
three similar genes, chlL, chlN and chlB are involved
in protochlorophyllide reduction during chlorophylls
biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB
exhibit significant sequence similarity to the nifH,
nifD and nifK subunits of nitrogenase, respectively.
Nitrogenase catalyzes the reductive formation of
ammonia from dinitrogen..
Length = 267
Score = 43.0 bits (101), Expect = 9e-05
Identities = 19/32 (59%), Positives = 24/32 (75%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
KGG+GK+TT+ NLS ALA G+ VL I DP+
Sbjct: 8 KGGIGKSTTSSNLSVALAKRGKKVLQIGCDPK 39
>gnl|CDD|48369 cd02040, NifH, NifH gene encodes component II (iron protein) of
nitrogenase. Nitrogenase is responsible for the
biological nitrogen fixation, i.e. reduction of
molecular nitrogen to ammonia. NifH consists of two
oxygen-sensitive metallosulfur proteins: the
mollybdenum-iron (alternatively, vanadium-iron or
iron-iron) protein (commonly referred to as component
1), and the iron protein (commonly referred to as
component 2). The iron protein is a homodimer, with an
Fe4S4 cluster bound between the subunits and two
ATP-binding domains. It supplies energy by ATP
hydrolysis, and transfers electrons from reduced
ferredoxin or flavodoxin to component 1 for the
reduction of molecular nitrogen to ammonia..
Length = 270
Score = 42.5 bits (100), Expect = 1e-04
Identities = 17/36 (47%), Positives = 28/36 (77%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
KGG+GK+TT NLS ALA +G+ V+++ DP+ +++
Sbjct: 9 KGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKADST 44
>gnl|CDD|73214 cd00550, ArsA_ATPase, Oxyanion-translocating ATPase (ArsA). This
ATPase is involved in transport of arsenite, antimonite
or other oxyanions across biological membranes in all
three kingdoms of life. ArsA contains a highly
conserved AAA motif present in the AAA+ ATPase
superfamily associated with a variety of cellular
activities. To form a functional ATP-driven pump, ArsA
interacts with the permease ArsB, which is a
channel-forming integral membrane protein. One of the
most interesting features of ArsA is the allosteric
activation by its transport substrates. A divalent
cation, typically Mg2+, is required for its enzymatic
activity..
Length = 254
Score = 41.8 bits (98), Expect = 2e-04
Identities = 44/202 (21%), Positives = 79/202 (39%), Gaps = 14/202 (6%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIE--LYDRKYSSYD-LLIEE 71
KGGVGKTT + + LA G+ VLL+ DP + S E + L E
Sbjct: 8 KGGVGKTTISAATAVRLAEQGKKVLLVSTDPAHSLSDSFNQEFGKGPTPVKGVENLSAME 67
Query: 72 KNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEK-----DRLFRLDKALSVQLTSDFSY 126
+ + L + L I + + L ++ IL E + + D+ +++
Sbjct: 68 IDPQEALEEYRQEVLEPIEANLLLEMLKGILEEELESPGIEEIAAFDEFSRYIDEAEYDV 127
Query: 127 IFLDCPP---SFNLLTM-NAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALD 182
+ D P + LL++ ++ A IL + F L + + + ++ E R + L
Sbjct: 128 VVFDTAPTGHTLRLLSLPTVLSWAREILSDPERTSFRLVCIPEKM-SLYETERAIQ-ELA 185
Query: 183 IQGIILTMFDSRNSLSQQVVSD 204
GI + L + V +
Sbjct: 186 KYGIDVDAVIVNQLLPEDVTNC 207
>gnl|CDD|177011 CHL00072, chlL, photochlorophyllide reductase subunit L.
Length = 290
Score = 41.6 bits (98), Expect = 2e-04
Identities = 18/32 (56%), Positives = 24/32 (75%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
KGG+GK+TT+ N+S ALA G+ VL I DP+
Sbjct: 8 KGGIGKSTTSCNISIALARRGKKVLQIGCDPK 39
>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function..
Length = 116
Score = 41.4 bits (97), Expect = 2e-04
Identities = 22/48 (45%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKY 62
KGGVGKTT A L+ LA G+ VL ID DP + L +E+ + K
Sbjct: 7 KGGVGKTTIAALLARYLAEKGKPVLAIDADP-DDLPERLSVEVGEIKL 53
>gnl|CDD|38036 KOG2825, KOG2825, KOG2825, Putative arsenite-translocating ATPase
[Inorganic ion transport and metabolism].
Length = 323
Score = 39.6 bits (92), Expect = 9e-04
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
KGGVGKTT + +L+ LA + E+VL+I DP N S
Sbjct: 27 KGGVGKTTCSCSLAVQLAKVRESVLIISTDPAHNLS 62
>gnl|CDD|111283 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam
family represents a conserved domain, which is
sometimes repeated, in an anion-transporting ATPase.
The ATPase is involved in the removal of arsenate,
antimonite, and arsenate from the cell.
Length = 304
Score = 39.3 bits (92), Expect = 0.001
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 15 KGGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
KGGVGKTT + + L+ G+ VLL+ DP + S
Sbjct: 9 KGGVGKTTVSCATAVRLSEQGKKVLLVSTDPAHSLS 44
>gnl|CDD|33438 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 39.0 bits (91), Expect = 0.001
Identities = 22/44 (50%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 15 KGGVGKTT-TAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL 57
KGGVGKTT A+ L L+ G NVL++D DP N LG+E
Sbjct: 8 KGGVGKTTIAALLLKRLLSKGGYNVLVVDADPDSNLPEALGVEE 51
>gnl|CDD|31343 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 39.1 bits (91), Expect = 0.001
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLIDLD 44
+ +A+ KGG GKTT A NL+ L ++L D D
Sbjct: 2 MQVAVASGKGGTGKTTVAANLAVLL-GDKYKLVLADCD 38
Score = 29.5 bits (66), Expect = 1.0
Identities = 24/128 (18%), Positives = 46/128 (35%), Gaps = 12/128 (9%)
Query: 126 YIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSALDIQG 185
+ +D + ++ AD ++ + F L L + LE VE G
Sbjct: 166 LLIIDSAAGTGCPVIASLKGADLAILVTEPTPFGLHDLKRALELVEHFGIPT-------G 218
Query: 186 IILTMFDSRNSLSQQVVSDVRKNLGGKVYNTVIPRNVRISEAPSYGKPAIIYDLKCAGSQ 245
I++ ++ +S ++ + G IP + I EA G+P + D K A +
Sbjct: 219 IVINRYNLGDSEIEEYCEE-----EGIPILGEIPYDKDIPEAYVNGEPFVEPDSKEAEAI 273
Query: 246 AYLKLASE 253
+
Sbjct: 274 LEEAEKLK 281
>gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain..
Length = 173
Score = 33.2 bits (76), Expect = 0.081
Identities = 43/193 (22%), Positives = 68/193 (35%), Gaps = 67/193 (34%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS--------TGLGIELYDRKYSSYDLL 68
GVGKTTTA L+ L G+ VLL+ D A+ +G+ +++ +
Sbjct: 10 GVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGVPVFEEGEGKDPVS 69
Query: 69 IE--------EKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRLFRLDKALSVQL 120
I E+N + +++ TA L I+ L E ++ R+ K
Sbjct: 70 IAKRAIEHAREENFDVVIVDTA-----------GRLQIDENLMEELKKIKRVVK------ 112
Query: 121 TSDFSYIFLDCPPSFNLLTMNAMAAADSILVPLQCEFFALEGLSQLLETVEEVRRTVNSA 180
P LL ++AM D++ + N A
Sbjct: 113 ------------PDEVLLVVDAMTGQDAV----------------------NQAKAFNEA 138
Query: 181 LDIQGIILTMFDS 193
L I G+ILT D
Sbjct: 139 LGITGVILTKLDG 151
>gnl|CDD|144749 pfam01268, FTHFS, Formate--tetrahydrofolate ligase.
Length = 555
Score = 32.8 bits (76), Expect = 0.11
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 17 GVGKTTTAINLSTALAAIGENV 38
G GKTTT I L AL +G+
Sbjct: 68 GEGKTTTTIGLGQALNRLGKKA 89
>gnl|CDD|73210 cd00477, FTHFS, Formyltetrahydrofolate synthetase (FTHFS)
catalyzes the ATP-dependent activation of formate ion
via its addition to the N10 position of
tetrahydrofolate. FTHFS is a highly expressed key
enzyme in both the Wood-Ljungdahl pathway of
autotrophic CO2 fixation (acetogenesis) and the glycine
synthase/reductase pathways of purinolysis. The key
physiological role of this enzyme in acetogens is to
catalyze the formylation of tetrahydrofolate, an
initial step in the reduction of carbon dioxide and
other one-carbon precursors to acetate. In purinolytic
organisms, the enzymatic reaction is reversed,
liberating formate from 10-formyltetrahydrofolate with
concurrent production of ATP..
Length = 524
Score = 32.0 bits (73), Expect = 0.18
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 17 GVGKTTTAINLSTALAAIGENV 38
G GKTTT I L+ AL A G+
Sbjct: 52 GEGKTTTTIGLAQALNAHGKKA 73
>gnl|CDD|36570 KOG1356, KOG1356, KOG1356, Putative transcription factor 5qNCA,
contains JmjC domain [Transcription].
Length = 889
Score = 31.1 bits (70), Expect = 0.32
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 6/87 (6%)
Query: 25 INLSTALAAIGENVLLIDLDPQGNASTGLGIELYDRKYSSYDLLIEEKNINQILIQTAIP 84
+NL++ L E + DL P+ + G+ E R + +L ++ + IL+ P
Sbjct: 649 LNLASKLP---EGFVRPDLGPKLYNAYGVSTE-LGRGDGTTNLHLDVSDAVNILVYVGEP 704
Query: 85 NLSI--IPSTMDLLGIEMILGGEKDRL 109
I I + + + + R+
Sbjct: 705 PGQIEQIAKVLKKIQEGDLDEITRSRI 731
>gnl|CDD|40027 KOG4830, KOG4830, KOG4830, Predicted sugar transporter
[Carbohydrate transport and metabolism].
Length = 412
Score = 28.9 bits (64), Expect = 1.4
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 50 STGLGIELYDRKYSSYDLLIEEKNINQILIQTAIPNLSIIPSTMDLLGIEMILGGEKDRL 109
S G+ +L + +YD L + I + +P ++ + + LL + GE+ R
Sbjct: 343 SNGIAYQLIELWTPAYDAL--KSAIFYRRVMVFVPGTCLVLAFLVLLSLAPFKIGERRRA 400
Query: 110 FRLDKAL 116
D+
Sbjct: 401 RPEDEQA 407
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 28.7 bits (65), Expect = 1.6
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 128 FLDCPPSFNLL--TMNAMAAADSILV 151
+D P + + T A+ AAD+ LV
Sbjct: 68 LIDTPGYADFVGETRAALRAADAALV 93
>gnl|CDD|114472 pfam05748, Rubella_E1, Rubella membrane glycoprotein E1. Rubella
virus (RV), the sole member of the genus Rubivirus
within the family Togaviridae, is a small enveloped,
positive strand RNA virus. The nucleocapsid consists of
40S genomic RNA and a single species of capsid protein
which is enveloped within a host-derived lipid bilayer
containing two viral glycoproteins, E1 (58 kDa) and E2
(42-46 kDa). In virus infected cells, RV matures by
budding either at the plasma membrane, or at the
internal membranes depending on the cell type and enters
adjacent uninfected cells by a membrane fusion process
in the endosome, directed by E1-E2 heterodimers. The
heterodimer formation is crucial for E1 transport out of
the endoplasmic reticulum to the Golgi and plasma
membrane. In RV E1, a cysteine at position 82 is crucial
for the E1-E2 heterodimer formation and cell surface
expression of the two proteins. The E1 has been shown to
be a type 1 membrane protein, rich in cysteine residues
with extensive intramolecular disulfide bonds.
Length = 496
Score = 28.6 bits (63), Expect = 1.8
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 219 PRNVRISEAPSYGKPAIIYDLKCAGSQAYLKLASE 253
PRNVR++ G PA++ L G +L + E
Sbjct: 356 PRNVRVTGCYQCGTPALVEGLAPGGGNCHLTVNGE 390
>gnl|CDD|31982 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 28.2 bits (63), Expect = 2.1
Identities = 12/30 (40%), Positives = 14/30 (46%)
Query: 9 ITIANQKGGVGKTTTAINLSTALAAIGENV 38
+ IA G GKTT + L AL G V
Sbjct: 3 VVIAGTSSGSGKTTVTLGLMRALRRRGLKV 32
>gnl|CDD|48077 cd01976, Nitrogenase_MoFe_alpha, Nitrogenase_MoFe_alpha_II:
Nitrogenase MoFe protein, beta subunit. A group of
proteins similar to the alpha subunit of the MoFe
protein of the molybdenum (Mo-) nitrogenase. The
nitrogenase enzyme catalyzes the ATP-dependent reduction
of dinitrogen to ammonia. The Mo-nitrogenase is the most
widespread and best characterized of these systems.
Mo-nitrogenase consists of the MoFe protein (component
1) and the Fe protein (component 2). MoFe is an
alpha2beta2 tetramer. Each alphabeta pair of MoFe
contains one P-cluster (at the alphabeta interface) and,
one molecule of iron molybdenum cofactor (FeMoco)
contained within the alpha subunit. The Fe protein
contains a single [4Fe-4S] cluster. Electrons are
transferred from the [4Fe-4S] cluster of the Fe protein
to the P-cluster of the MoFe and in turn to FeMoCo, the
site of substrate reduction..
Length = 421
Score = 28.3 bits (63), Expect = 2.2
Identities = 29/107 (27%), Positives = 44/107 (41%), Gaps = 25/107 (23%)
Query: 75 NQILIQTAIPNLSIIPSTMDLLGIEMILGGEK---------DRLFRLDKALSVQLTSDFS 125
N +T + N + T D +++ GG+K LF L+K +SVQ
Sbjct: 53 NYYRGETGVDNFGTMQFTTDFQEKDIVFGGDKKLAKAIDEAYELFPLNKGISVQSE---- 108
Query: 126 YIFLDCPPSFNLLTMNAMAAADS-----ILVPLQCEFFALEGLSQLL 167
CP + A+A S +VP++CE F G+SQ L
Sbjct: 109 -----CPVGLIGDDIEAVARKASKELGIPVVPVRCEGF--RGVSQSL 148
>gnl|CDD|32626 COG2759, MIS1, Formyltetrahydrofolate synthetase [Nucleotide
transport and metabolism].
Length = 554
Score = 28.3 bits (63), Expect = 2.4
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 17 GVGKTTTAINLSTALAAIGENVLL 40
G GKTTT I L AL +G+ ++
Sbjct: 66 GEGKTTTTIGLVDALNKLGKKAII 89
>gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 473
Score = 28.1 bits (63), Expect = 2.8
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 173 VRRTVNSALDIQGIILTMFDSRNSLSQQVV 202
VR+ +N A+D GI+ +F + + Q+V
Sbjct: 249 VRKALNLAIDRDGIVGALFGGQGRPATQLV 278
>gnl|CDD|36746 KOG1533, KOG1533, KOG1533, Predicted GTPase [General function
prediction only].
Length = 290
Score = 27.9 bits (62), Expect = 3.2
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLDP 45
G GK+T +S L+AIG V +++LDP
Sbjct: 12 GSGKSTYCNGMSQFLSAIGRPVAVVNLDP 40
>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is
unkown. The protein sequences are similar to the ArgK
protein in E. coli. ArgK protein is a membrane ATPase
which is required for transporting arginine, ornithine
and lysine into the cells by the arginine and ornithine
(AO system) and lysine, arginine and ornithine (LAO)
transport systems..
Length = 148
Score = 27.5 bits (61), Expect = 4.1
Identities = 15/37 (40%), Positives = 20/37 (54%)
Query: 16 GGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTG 52
G GK+T L TAL A G+ V ++ +DP S G
Sbjct: 8 PGAGKSTLIDALITALRARGKRVAVLAIDPSSPFSGG 44
>gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the
bacterial RecA. The precise function of radB is
unclear..
Length = 218
Score = 27.2 bits (60), Expect = 5.0
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 7 RIITIANQKGGVGKTTTAINLSTALAAIGENVLLID 42
+T G GKT AI L+ A G+ V ID
Sbjct: 19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID 54
>gnl|CDD|30887 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 27.0 bits (60), Expect = 5.5
Identities = 14/30 (46%), Positives = 17/30 (56%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLDPQ 46
G GKTTTA L+ L G+ VLL+ D
Sbjct: 110 GSGKTTTAGKLAKYLKKKGKKVLLVAADTY 139
>gnl|CDD|33690 COG3903, COG3903, Predicted ATPase [General function prediction
only].
Length = 414
Score = 26.8 bits (59), Expect = 6.6
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 16 GGVGKTTTAINLSTALAAIGENVLLIDLDPQGNAS 50
GGVGKTT A+ + A + + V +DL P + +
Sbjct: 23 GGVGKTTLALQAAHAASEYADGVAFVDLAPITDPA 57
>gnl|CDD|147155 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 103
Score = 26.8 bits (60), Expect = 7.0
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLI----DLDPQ 46
G GKT TA L L + VL + DL Q
Sbjct: 28 GSGKTLTAAKLIARLLKGKKKVLFLVPRKDLLEQ 61
>gnl|CDD|144151 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 26.7 bits (60), Expect = 7.3
Identities = 13/28 (46%), Positives = 16/28 (57%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLD 44
G GKTTT L+ L G+ VLL+ D
Sbjct: 11 GSGKTTTIAKLAAYLKKQGKKVLLVAAD 38
>gnl|CDD|37016 KOG1805, KOG1805, KOG1805, DNA replication helicase [Replication,
recombination and repair].
Length = 1100
Score = 26.5 bits (58), Expect = 7.5
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLI 41
G GKTTT L L A+G+ VLL
Sbjct: 695 GTGKTTTISLLIKILVALGKKVLLT 719
>gnl|CDD|30875 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 26.4 bits (58), Expect = 7.6
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL 57
G GK+T A L L A G +V L+D D N GL +L
Sbjct: 33 GSGKSTIANALEEKLFAKGYHVYLLDGD---NVRHGLNRDL 70
>gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea..
Length = 187
Score = 26.4 bits (58), Expect = 7.7
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 17 GVGKTTTAINLSTALAAIGENVLLIDLD 44
G GKTT A+ A A GE L + L+
Sbjct: 9 GTGKTTFALQFLYAGLARGEPGLYVTLE 36
>gnl|CDD|30999 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and
related FAD-dependent oxidoreductases [Coenzyme
metabolism / Energy production and conversion].
Length = 387
Score = 26.2 bits (57), Expect = 8.7
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 4/42 (9%)
Query: 16 GGVGKTTTAINLSTALAAIGENVLLIDLDPQGNASTGLGIEL 57
G A+ ALA G +V L++ P+ G GI L
Sbjct: 10 AGPAGLALAL----ALARAGLDVTLLERAPRELLERGRGIAL 47
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.317 0.135 0.365
Gapped
Lambda K H
0.267 0.0509 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,905,529
Number of extensions: 148420
Number of successful extensions: 454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 435
Number of HSP's successfully gapped: 86
Length of query: 265
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 173
Effective length of database: 4,275,709
Effective search space: 739697657
Effective search space used: 739697657
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.9 bits)